[BioC] getGene type not recognized

[Steffen Durinck]

Dear John,

Thank you for reporting this.  It looks like Ensembl migrated to a new version overnight and changed the attribute hgnc_symbol to hgnc without informing us. getGene has hgnc_symbol hardcoded in it and thus won't work.  I would recommend to do your query using the more general getBM function.  Meanwhile I'll update the getGene function asap.

As you suggested, you can do the query via getBM and this is the recommended way as it works with all versions of Ensembl, here's how:

getBM(c("affy_hg_u95av2","hgnc","ensembl_gene_id","chromosome_name","start_position","end_position","strand","description"), filters="affy_hg_u95av2", values="1939_at", mart=mart)

Cheers,
Steffen

----- Original Message -----
From: John Lande <john.lande77 at gmail.com>
Date: Thursday, October 25, 2007 4:00 am
Subject: Re: [BioC] getGene type not recognized
To: bioconductor at stat.math.ethz.ch

> maybe I found the problems, but I will not be able to solve the issue:
> 
> if I run the getBM command, everything works but if in the 
> attributes i put
> the field hgnc_symbol, it complains with the same error:
> 
> Error in getBM(attributes = c("affy_hg_u95av2", "hgnc_symbol",
> "chromosome_name",  :
> Invalid attribute(s): hgnc_symbol
> Please use the function 'listAttributes' to get valid attribute names
> 
> if I run 'listAttributes' there is no hgnc_symbol, but hgnc. it is 
> possiblethat by default getGene still have this parameter ad default.
> 
> 
> On 10/25/07, John Lande <john.lande77 at gmail.com> wrote:
> >
> > Dear BioC,
> >
> >
> > I have the following problem with biomaRt packages:
> >
> > if I run any script with the function getGene, it seems it cannot
> > recognize the type field.
> >
> > it happen also with the example in the man of getGene:
> >
> > >mart = useMart("ensembl", dataset="hsapiens_gene_ensembl")
> > >g = getGene( id = "1939_at", type = "affy_hg_u95av2", mart = mart)
> > >show(g)
> > Error in getBM(attributes = attrib, filters = type, values = id, 
> mart =
> > mart) :
> > Invalid attribute(s): hgnc_symbol
> > Please use the function 'listAttributes' to get valid attribute 
> names>
> > in general I am having problems with this packages in these day, 
> when I am
> > using long input. I handled this using shorter input, and then 
> merging the
> > results, but now I dont know what to do.
> >
> > by the way I am running ubuntu 7.04.
> >
> > did someone have the notice the same?
> >
> >
> >
> > > sessionInfo()
> > R version 2.6.0 (2007-10-03)
> > x86_64-unknown-linux-gnu
> >
> > locale:
> > LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-
> 8;LC_COLLATE=en_US.UTF-8;LC_MONETARY=en_US.UTF-
> 8;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_US.UTF-
> 8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8;LC_IDENTIFICATION=C
> >
> >
> > attached base packages:
> > [1] tools     stats     graphics  grDevices utils     datasets  
> methods> [8] base
> >
> > other attached packages:
> > [1] Biobase_1.17.0        biomaRt_1.12.0        RCurl_0.8-3
> > [4] mouseLLMappings_2.0.1
> >
> > loaded via a namespace (and not attached):
> > [1] rcompgen_0.1-17 XML_1.93-2
> >
> >
> >
> > thank you
> >
> 
> 	[[alternative HTML version deleted]]
> 
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